The prison disallows any deviation from military grooming regulations. Manning was in genpop, and repeatedly violated this regulation growing out hair/wearing makeup ect so the prison kept pulling her privileges, plus getting Manning thrown back in adseg as punishment. This is what all prisons do when you get written up for minor violations of dress code, after there's nothing left to restrict they just put you in solitary.
tl;dr Manning has won the right to transition to female while being incarcerated through a lawsuit but the military doesn't know how to accomodate this. I'm guessing Manning will get moved to one of the empty wings at Leavenworth, and effectively be in solitary confinement with an entire wing to herself. That will be the prison's concession, we have complied with the lawsuit so here's your new prison to yourself as punishment because there exists no political directives from Washington DC and the military can only follow it's own rulebook.
EDIT: I don't know why I am being downvoted. Gitmo has shown that the military is more than willing to force-feed someone.